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Sample GSM1048172 Query DataSets for GSM1048172
Status Public on Mar 06, 2013
Title Buccal cell 18m twin 1, B1072
Sample type genomic
Source name Buccal cheek swab, DZ, 18 months
Organism Homo sapiens
Characteristics gender: female
age: 18 months
cell type: normal buccal cells
monozygotic: 0
dizygotic: 1
monochorionic: 0
sibship: 10
twin: 1
Extracted molecule genomic DNA
Extraction protocol gDNA was purified from buccal swabs using phenol chloroform extraction.
Label Cy5 and Cy3
Label protocol Bisulphite conversion was carried out using the Methyl Xceed bisulphite kit as per the manufacturer's instructions.
Hybridization protocol Bisulphite-converted DNA was amplified, fragmented and hybridised to the Illumina Infinium Human Methylation27 BeadChip using the standard llumina protocol.
Scan protocol Arrays were imaged using the BeadArray Reader using the standard recommended Illumina scanner setting.
Description B1072.1_18m
Data processing Data were preprocessed using the Bioconductor Minfi package in R by the 'illumina' method and normalized to control probes. Subset quantile normalization was performed on type 1 and type 2 probes. Probes failing P detection cutoff of <0.01 were removed. Probes on the X and Y chromosomes have been removed from the processed data. Outlier samples were removed. Between-array quantile normalization was performed to arrive at the final data set of 330168 probes and 53 samples.
Submission date Dec 03, 2012
Last update date Mar 06, 2013
Contact name David Martino
Phone 0863191635
Organization name Telethon Kids Institute
Street address Perth Childrens Hospital, 15 Hospital Avenue
State/province Western Australia
ZIP/Postal code 6009
Country Australia
Platform ID GPL13534
Series (1)
GSE42700 Epigenome analysis of buccal cells from monozygotic and dizygotic twins

Data table header descriptions
VALUE Quantile-normalized average Beta

Data table
cg00000957 0.8888531344941
cg00001349 0.840200976024714
cg00001583 0.0452818472975659
cg00002028 0.0559563063001833
cg00003202 0.0234573950810811
cg00003287 0.0565942676129305
cg00004121 0.600048558594553
cg00007036 0.961324854690061
cg00007898 0.0334879462525743
cg00008004 0.104026628427576
cg00008647 0.0599949303790107
cg00009292 0.166829783278491
cg00009916 0.0229979021962698
cg00011717 0.933016064524596
cg00014168 0.698156202831102
cg00015286 0.765040442513946
cg00015930 0.97284055184092
cg00016238 0.746108905198464
cg00017221 0.0445078868625457
cg00017437 0.0197751493921081

Total number of rows: 330168

Table truncated, full table size 9442 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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